Aminoacyl tRNA Synthetase



Aminoacyl tRNA synthetase (aaRS) catalyzes the esterification of a specific amino acid to its cognate tRNA to form an aminoacyl-tRNA. The amino acid is transferred by the ribosome from the aminoacylated-tRNA onto a growing polypeptide chain. Class I of aaRS is a monomer or dimer, it has 2 highly conserved sequence motifs and it aminoacylates at the 2’-OH of an adenosine nucleotide. Class II of aaRS is a dimer or tetramer, it has 3 highly conserved sequence motifs and it aminoacylates at the 3’-OH of an adenosine nucleotide. CP1 domain of RS edits a mischarged aa-tRNA. Some of the crystal structures are complexes of the RS with their reactant analog: amino acid-sulfamoyl adenine (aa-SA).

3D Structures of Aminoacyl tRNA synthetase
Class I aaRS

Arg-RS
1bs2 – yArgRS

3gdz – ArgRS residues 1-106 – Klebsiella pneumoniae

1iq0 – TtArgRS - Thermus thermophilus

Arg-RS + tRNA 2zuf - PhArgRS + tRNA-Arg - Pyrococcus horikoshii

1f7v - yArgRS + Arg-tRNA

Arg-RS ternary complex 1f7u – yArgRS + Arg-tRNA + Arg

2zue – PhArgRS + tRNA-Arg + ATP analog

Cys-RS
1li5 - EcCysRS - Escherichia coli

1li7 - EcCysRS + Cys

1u0b – EcCysRS + Cys-tRNA

Gln-RS
1nyl– EcGlARS

1qrt, 1qru - EcGlARS (mutant) + Gln-tRNA

1gtr, 1gts,  1gsg - EcGlARS + Gln-tRNA

Gln-RS ternary complex 1euq, 1euy – EcGlARS + Gln-tRNA + Gln-SA

1exd - EcGlARS + Gln-tRNA (mutant) + AMP

Glu-RS
1gln – TtGluRS

2o5r - TmGluRS

3aii – GluRS – Methanothermobacter thermautotrophicus

2ja2 – MtGluRS – Mycobacterium tuberculosis

2zlz – EcGluRS

2hz7 – DrGluRS – Deinococcus radiodurans

2hra – yGluRS N-terminal Glu-RS + small substrates or analogs 3afh - TmGluRS + Glu-AMP analog

2rd2, 2re8 – EcGluRS (mutant) + Glu-SA

2cuz – TtGluRS + Glu

1j09 - TtGluRS + Glu + ATP

1n75 - TtGluRS + ATP

2fco - GluRS residues 2-485 + Glu – Synechococcus elongates

Glu-RS + tRNA 1zjw – EcGluRS + Glu-tRNA

Glu-RS ternary complex 3akz, 3al0 – TmGluRS + tRNA + Glu-AMP analog – Thermotoga maritime

1o0b, 1o0c - EcGluRS + Glu-tRNA + Glu + AMP 2cv0, 1n77 - TtGluRS + Glu + Glu-tRNA

1n78 - TtGluRS + Glu-ol + Glu-tRNA

2cv1 - TtGluRS + Glu-ol + ATP + Glu-tRNA

2cv2 - TtGluRS + Glu-SA + Glu-tRNA

2hrk, 2hsm - yGluRS N-terminal + GU4 nucleic-binding protein 1

Ile-RS
1ile - TtIleRS

1wny, 1udz – TtIleRS editing domain

Ile-RS + small substrates or analogs

1ue0 - TtIleRS editing domain + Val

1wnz - TtIleS editing domain + Val-adenylate

1wk8 - TtIleRS editing domain + Val-SA

1jzq – TtIleS + Ile-adenylate analog

1jzs – TtIleS + antibiotic

Ile-RS ternary complex

1ffy, 1qu2,  1qu3 - SaIleRS + Ile-tRNA + antibiotic - Staphylococcus aureus

Leu-RS
3o0a – AaLeuRS hydrolytic domain – Aquifex aeolicus 2wfd – hLeuRS editing domain – human

2wfe - CaLeuRS editing domain – Candida albicans

2ajg - EcLeuRS editing domain

1wkb – PhLeuRS residues 1-810

Leu-RS + small substrates or analogs

2wfg - CaLeuRS editing domain + benzoxaborole-AMP

2v0c – TtLeuRS + Leu-SA + benzoxaborole-AMP

1h3n - TtLeuRS + Leu-SA

1obc, 1obh – TtLeuRS + substrate analog

2ajh, 2aji - EcLeuRS editing domain + aa

Leu-RS + tRNA

1wz2 – PhLeuRS Leu-tRNA

Leu-RS ternary complex

2v0g - TtLeuRS + Leu-tRNA + benzoxaborole-AMP

2bte, 2byt - TtLeuRS + Leu-tRNA + Leu

Lys-RS
1irx – PhLysRS

1bbw – EcLysRS

1krs, 1krt – EcLysRS anticodon-binding domain – NMR 3dsq – DhLysRS – Desulfitobacterium hafniense

2e3c - MmLysRS catalytic domain - Methanosarcina mazei

3bju – hLysRS residues 70-579

Lys-RS + small substrates or analogs

3a74 – GsLysRS + diadenosine tetraphosphate – Geobacillus stearothermophilus

3e9h, 3e9i – BsLysRS + Lys-SA - Bacillus stearothermophilus

2zin – MmLysRS catalytic domain + Boc-Lys + ATP analog

2zio - MmLysRS catalytic domain + Aloc-Lys-AMP + PNP

2zcd - MmLysRS catalytic domain + AMPPNP

2zce - MmLysRS catalytic domain + pyrro-Lys + ATP analog

2zim - MmLysRS residues 185-454+ pyrro-Lys-adenylate

2q7e - MmLysRS C-terminal + ATP analog

2q7g - MmLysRS C-terminal+ pyrro-Lys analog+ ATP

1bbu, 1e10,  1lyl – EcLysRS + Lys

1e1t - EcLysRS + Lys-adenylate

1e22 - EcLysRS + Lys + AMPPCP

1e24 - EcLysRS + Lys + ATP

Leu-RS + tRNA

2zni, 2znj – DhLysRS + tRNA

Met-RS
1a8h – TtMetRS 1med – EcMetRS Zinc-binding domain - NMR

1qqt - EcMetRS residues 2-552

2x1l - MsMetRS residues 2-515 – Mycobacterium smegmatis

3h97 – EcMetRS residues 2-548 (mutant)

3h9c - EcMetRS residues 2-548

2d54, 2d5b – TtMetRS (mutant)

1woy – TtMetRS residues 1-500 (mutant)

2djv – hMetRS WHEP-TRS domain – NMR

1pyb – AaMetRS β subunit

1rqg – PaMetRS – Pyrococcus abyssi

1mkh – PaMetRS C-terminal

Met-RS + small substrates or analogs

3kfl – LmMetRS residues 206-747+ Met-adenylate - Leishmania major

2x1m - MsMetRS residues 2-515 + Met

1p7p, 1pfu,  1pfv,  1pfw - EcMetRS residues 2-548 + Met

1pfy - EcMetRS residues 1-551 + Met-SA

1f4l - EcMetRS residues 1-551 + Met

1pg0 - EcMetRS residues 1-551 + Met-adenylate

1pg2 - EcMetRS residues 1-551 + Met + adenine

3h99 - EcMetRS residues 2-548 (mutant) + Met

3h9b - EcMetRS residues 2-548 (mutant) + azidonorleucine

Met-RS + tRNA 2csx – AaMetRS + Met-tRNA

Met-RS + tRNA

2ct8 - AaMetRS + Met-tRNA + Met-SA

2dxi – TtMetRS + tRNA + ATP + Glu-ol

2hsn - yMetRS N-terminal + GU4 nucleic-binding protein 1 N-terminal

Trp-RS
1d2r - GsTrpRS

3prh – TrpRS (mutant) – Bacillus subtilis

3n9i – TrpRS – Yarsinia pestis

3m5w – TrpRS – Campylobacter jejuni

3a04 – ApTrpRS – Aeropyrum pernix

3hzr – EhTrpRS – Entamoeba histolytica

3i05 – TbTrpRS residues 3-389 – Trypanosoma brucei

3hv0 – TRrpS residues 206-593 – Cryptosporidium parvum

3foc – GlTrpRS – Giardia lamblia

1o5t – hTrpRS catalytic fragment

1ulh – hTrpRS residues 35-424

2el7 – TtTrpRS

2ip1, 3kt0 – yTrpRS – yeast

2yy5 – TrpRS – Mycoplasma pneumoniae

2g36 – TmTrpRS Trp-RS + small substrates or analogs

3a05 – ApTrpRS + Trp

3kt3 – yTrpRS + Trp-adenylate

3kt6, 3kt8 – yTrpRS + Trp

3jxe – PhTrpRS + Trp-adenylate

3fhj, 3fio – BsTrpRS + Trp + AMP + Pi

2quh – hTrpRS + Trp

2qui - hTrpRS + Trp-amide + ATP

2quj - hTrpRS + Trp-adenylate

2quk – hTrpRS + ATP

2ov4 – GsTrpRS + adenosine tetraphosphate

1i6k, 1i6l,  1i6m – GsTrpRS + Trp-adenylate

1yid, 2a4m – DrTrpRS + ATP

1yi8, 1yia – DrTrpRS + Trp

1mau – GsTrpRS + Trp + ATP

1maw, 1m83 - GsTrpRS + ATP

1mb2 - GsTrpRS + Trp

Trp-RS + tRNA

2azx – hTrpRS (mutant) + tRNA

2ake, 2dr2 - hTrpRS + Trp-tRNA

Tyr-RS
1tya, 1tyb,  1tyc,  1tyd,  2ts1 – GsTyrRS

3qe4, 3d6u,  3d6v,  2pxh,  2hgz,  1u7d – MjTyrRS – Methanocaldococcus jannaschii

1u7x - MjTyrRS (mutant)

2jan – MtTyrRS

1y42 - NcTyrRS – Neurospora crassa

2cya – ApTyrRS

1n3l - hTyrRS residues 1-364

1r6t, 1r6u – yTyrRS (mutant)

1jh3 – GsTyrRS C-terminal – NMR

Tyr-RS + small substrates or analogs

3ts1 – GsTyrRS + Tyr-adenylate intermediate

4ts1 – GsTyrRS + Tyr

3p0h, 3p0i,  3p0j – LmTyrRS + inhibitor

3n2y – MjTyrRS + tetrazolyl phenylalanine

2zp1 – MjTyrRS (mutant) + Tyr

1zh0 - MjTyrRS (mutant) + naphthyl-Ala

1zh6 - MjTyrRS (mutant) + acetyl-Phe

2ag6 - MjTyrRS (mutant) + bromo-Phe

2yxn – EcTyrRS residues 1-322 + azido-Tyr

1vbm – EcTyrRS + Tyr-SA

1vbn – EcTyrRS (mutant) + Tyr-SA

1wq3, 1wq4 - EcTyrRS (mutant) + Tyr

1x8x – EcTyrRS + Tyr 2pid – hTyrRS residues 28-375 + Tyr-SA

2j5b – TyrRS residues 2-346 + Tyr-ol – Acanthamoeba polyphaga minivirus

2dlc – yTyrRS + tRNA + Tyr-SA

2cyb – AfTyrRS + Tyr - Archaeoglobus fulgidus

2cyc – PhTyrRS + Tyr

1q11 – hTyrRS residues 1-364 + Tyr-ol

1h3e - TtTyrRS + Tyr-tRNA + Tyr-ol + ATP

1h3f - TtTyrRS + Tyr-ol

1jh3 – GsTyrRS C-terminal – NMR

1jii, 1jij,  1jil – SaTyrRS + inhibitor

Tyr-RS + tRNA

1j1u – MjTyrRS + Tyr-tRNA

2rkj – NcTyrRS + RNA

Val-RS
1iyw - TtValRS

1wk9, 1wka – TtValRS CP1 domain

Val-RS ternary complex

1ivs – TtValRS + Val-SA + Val-tRNA

1gax - TtValRS + Val-adenylate analog + Val-tRNA Class II aaRS

Ala-RS
3g98 – AaAlaRS residues 758-867

1riq - AaAlaRS catalytic fragment

2zze, 2zzf,  1wnu,  1wxo,  1v4p – PhAlaRS

2zvf – AfAlaRS C-terminal

Ala-RS + small substrates or analogs

3hxu, 3hxv,  3hxw – EcAlaRS catalytic fragment + aa-adenylate

3hxz, 3hy0,  3hy1 - EcAlaRS catalytic fragment (mutant) + aa-adenylate

3hxx - EcAlaRS catalytic fragment + AMPPCP

3hxy - EcAlaRS catalytic fragment + AMPPCP + Ala-AMP + PCP

3htz - AaAlaRS residues 2-454 + Ser

1yfr – AaAlaRS + ATP

1yfs – AaAlaRS + Ala

1yft, 1ygb - AaAlaRS catalytic fragment + aa

2zzg - PhAlaRS + Ala-SA

2ztg – AfAlaRS + Ala-SA

Asp-RS
3nen, 1b8a – TkAspRS - Thermococcus kodakarensis

3i7f – EhAspRS

1wyd– AspRS – Sulfolobus tokodaii

1eov - yAspRS

1n9w, 1l0w,  1g51 – TtAspRS

1eqr – EcAspRS

Asp-RS + small substrates or analogs

3nel – TkAspRS + Asp

3nem - TkAspRS + Asp-adenylate

Asp-RS + tRNA

3kfu, 1efw – TtAspRS + tRNA

1asy, 1asz – yAspRS + Asp-tRNA

Asp-RS ternary complex

1il2, 1c0a – EcAspRS + Asp-tRNA + Asp-adenylate

Asn-RS
1x56 - PhAsnRS

2kqr – BmAsnRS N-terminal – NMR – Brugia malayi Asn-RS + small substrates or analogs

2xti – BmAsnRS catalytic fragment + Asn-adenine analog

2xgt - BmAsnRS catalytic fragment + Asn-SA

1x54 – PhAsnRS + Asn-adenylate

1x55 - PhAsnRS + Asn-SA

11as – EcAsnRS + Asn

12as - EcAsnRS + Asn + AMP

Gly-RS
1ati – TtGlyRS

2q5h – hGlyRS residues 55-739

2q5i - hGlyRS residues 55-739 (mutant)

2pme – hGlyRS

2pmf – hGlyRS (mutant)

1j5w – TmGlyRS α chain

Gly-RS + small substrates or analogs

2zt5, 2zxf – hGlyRS residues 55-739 + bis-adenosine tetraphosphate

2zt6 - hGlyRS residues 55-739 + AMPCPP

2zt7 - hGlyRS residues 55-739 + Gly + ATP

2zt8 - hGlyRS residues 55-739 + Gly-AMP analog

1b76 – TtGlyRS + ATP

1ggm – TtGlyRS + Gly-adenylate

His-RS
1htt - EcHiusRS

3net – HisRS – Nostoc

1h4v – TtHisRS

1qe0 – SaHisRS

3hri – TbHisRS

1wu7 – HisRS – Thermoplasma acidophilum

1x59 – hHisRS WHEP-TRS domain - NMR

His-RS + small substrates or analogs

3lc0 – HisRS residues 45-478 + His – Trypanosoma cruzi

1adj – TtHisRS + His

3hrk - TbHisRS + His-adenylate

2el9 - EcHisRS + His-SA

1kmm, 1ady - EcHisRS + His-adenylate

1kmn - EcHisRS + His-ol + ATP

Phe-RS
1pys – TtPheRS

3l4g, 3cmq – hPheRS

2cxi – PhPheRS β chain N-terminal 3ica – PheRS β chain – Porphyromonas gingivalis Phe-RS + small substrates or analogs

3pco – EcPheRS + phenylalanine+ AMP

3hfz, 2amc – TtPheRS α+β chains + Tyr

2akw, 1b70 - TtPheRS α+β chains + Phe

1jjc, 1b7y - TtPheRS α+β chains + Phe-adenylate

2aly - TtPheRS α+β chains + Phe-SA

2rhq, 2rhs – PheRS α+β chains (mutant) + inhibitor – Staphylococcus haemolyticus

Phe-RS + small substrates or analogs

1eiy - TtPheRS α+β chains + Phe-tRNA

Phe-RS + small substrates or analogs

2iy5 - TtPheRS α+β chains + Phe-ol + Phe-tRNA

Pro-RS
1hc7 – TtProRS

2i4l – RpProRS – Rhodopseudomonas palustris

1nj2 - MtProRS – Methanothermobacter thermautotrophicus

1nj8 – MjProRS

Pro-RS + small substrates or analogs

3ial – GlProRS residues 34-542 + Pro-adenylate

2i4m, 2i4n – RpProRS + aa-SA

2i4o – RpProRS + ATP

2j3l – EfProRS + Pro-SA – Enterococcus faecalis

2j3m – EfProRS + Pro-ol + ATP

1nj1, 1nj5,  1nj6 – MtProRS + aa-SA

1h4t - TtProRS + Pro

Pro-RS ternary complex

1h4q - TtProRS + Pro-tRNA + Pro-ol

1h4s - TtProRS + Pro-tRNA + Pro-SA

Ser-RS
3lsq – TbSerRS

1sry - TtSerRS

3err – TtSerRS/dynein heavy chain

2zr3 – PhSerRS

2dq3 – AaSerRS

2du7 – MjSerRS

2odr – SerRS – Methanococcus maripaludis

2cim – MbSerRS – Methanosarcina barkeri

1wle – SerRS – bovine Ser-RS + small substrates or analogs

2zr2 – PhSerRS + ATP

2dq0 – PhSerRS + Ser-SA

2cj9 – MbSerRS + Ser-SA

2cjb – MbSerRS + Ser

2cja – MbSerRS + ATP

1ses, 1set – TtSerRS + Ser-adenylate analog

3lss – TbSerRS + ATP

Ser-RS + tRNA

1ser – TtSerRS + Ser-tRNA

2du4 - AfSerRS + Cys-tRNA

Ser-RS ternary complex

2du3 – AfSerRS + Cys-tRNA + phosphoserine

2du5, 2du6 - AfSerRS (mutant) + Cys-tRNA + phosphoserine

Thr-RS
1y2q - PaThrRS editing domain

1wwt – hThrRS TGS domain – NMR

1tje - EcThrRS editing domain Thr-RS + small substrates or analogs

3pd2, 3pd3,  3pd4,  3pd5 – PaThrRS editing domain + aa-aminoadenosine

2hkz – PaThrRS editing domain + Ser

2hl0, 2hl1 - PaThrRS editing domain + Ser-adenylate

2hl2 - PaThrRS editing domain + Ser-SA

1tke - EcThrRS editing domain + Ser

1tkg - EcThrRS editing domain + Ser-SA

1tky - EcThrRS editing domain + Ser-adenylate

1fyf, 1evl - EcThrRS catalytic and anticodon-binding domains + aa-SA

1evk - EcThrRS catalytic and anticodon-binding domains + Thr

1nyq – SaThrRS + Thr-SA

1nyr – SaThrRS + ATP

Thr-RS + tRNA

1qf6 – EcThrRS + Thr-tRNA

1kog – EcThrRS catalytic and anticodon-binding domains + mRNA